diff --git a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/README.md b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/README.md index de38cabf8..c607be07b 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/README.md +++ b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/README.md @@ -10,7 +10,7 @@ A GTN has been developed for this workflow. [https://training.galaxyproject.org/ ### Search Databases (FASTA) from [Zenodo](https://zenodo.org/records/14181725) - `HUMAN SwissProt Protein_Database.fasta` -- `Species UniProt FASTA.fasta` +- `Species UniProt Protein Database FASTA.fasta` - `Contaminants (cRAP) Protein Database.fasta` ### MSMS files download from [Zenodo](https://zenodo.org/records/14181725) - `PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.mgf` diff --git a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation-tests.yml b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation-tests.yml index ec1cf46c2..2b485cddd 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation-tests.yml +++ b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation-tests.yml @@ -1,18 +1,18 @@ - doc: Test outline for iwc-clinicalmp-database-generation job: - HUMAN-SwissProt-Protein-Database: + Human SwissProt Protein Database: class: File location: https://zenodo.org/records/14181725/files/HUMAN-SwissProt-Protein-Database.fasta?download=1 filetype: fasta - Species_UniProt_FASTA: + Species UniProt Protein Database: class: File location: https://zenodo.org/records/14181725/files/Species_UniProt_FASTA.fasta?download=1 filetype: fasta - Contaminants-cRAP-Protein-Database: + Contaminants cRAP Protein Database: class: File location: https://zenodo.org/records/14181725/files/Contaminants(cRAP)-Protein-Database.fasta?download=1 filetype: fasta - Input-MGF-files: + Tandem Mass Spectrometry (MS/MS) datasets: class: Collection collection_type: list elements: @@ -37,7 +37,7 @@ asserts: - that: has_text text: ">sp|" - CSV database: + Metanovo Compact CSV database: asserts: - that: has_text text: "index Accession" diff --git a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation.ga b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation.ga index 0ca4414cf..bbe7e3a9f 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation.ga @@ -18,18 +18,18 @@ }, "steps": { "0": { - "annotation": "HUMAN-SwissProt-Protein-Database", + "annotation": "Human SwissProt Protein Database", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "HUMAN-SwissProt-Protein-Database", - "name": "HUMAN-SwissProt-Protein-Database" + "description": "Human SwissProt Protein Database", + "name": "Human SwissProt Protein Database" } ], - "label": "HUMAN-SwissProt-Protein-Database", + "label": "Human SwissProt Protein Database", "name": "Input dataset", "outputs": [], "position": { @@ -45,18 +45,18 @@ "workflow_outputs": [] }, "1": { - "annotation": "Input-MGF-files", + "annotation": "Tandem Mass Spectrometry (MS/MS) datasets", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Input-MGF-files", - "name": "Input-MGF-files" + "description": "Tandem Mass Spectrometry (MS/MS) datasets", + "name": "Tandem Mass Spectrometry (MS/MS) datasets" } ], - "label": "Input-MGF-files", + "label": "Tandem Mass Spectrometry (MS/MS) datasets", "name": "Input dataset collection", "outputs": [], "position": { @@ -72,18 +72,18 @@ "workflow_outputs": [] }, "2": { - "annotation": "Species_UniProt_FASTA", + "annotation": "Species UniProt Protein Database", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Species_UniProt_FASTA", - "name": "Species_UniProt_FASTA" + "description": "Species UniProt Protein Database", + "name": "Species UniProt Protein Database" } ], - "label": "Species_UniProt_FASTA", + "label": "Species UniProt Protein Database", "name": "Input dataset", "outputs": [], "position": { @@ -99,18 +99,18 @@ "workflow_outputs": [] }, "3": { - "annotation": "Contaminants-cRAP-Protein-Database", + "annotation": "Contaminants cRAP Protein Database", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "Contaminants-cRAP-Protein-Database", - "name": "Contaminants-cRAP-Protein-Database" + "description": "Contaminants cRAP Protein Database", + "name": "Contaminants cRAP Protein Database" } ], - "label": "Contaminants-cRAP-Protein-Database", + "label": "Contaminants cRAP Protein Database", "name": "Input dataset", "outputs": [], "position": { @@ -233,7 +233,7 @@ "post_job_actions": { "RenameDatasetActionoutput_csv": { "action_arguments": { - "newname": "CSV database" + "newname": "Metanovo Compact CSV database" }, "action_type": "RenameDatasetAction", "output_name": "output_csv" @@ -265,7 +265,7 @@ "uuid": "02940034-f0fe-4151-acd0-c6982e77b717" }, { - "label": "CSV database", + "label": "Metanovo Compact CSV database", "output_name": "output_csv", "uuid": "d7208cb6-a907-4a8b-b8b7-cf44c103d14a" }